[gmx-users] Re: cannot read frames out from trr files

[Justin Lemkul]

On 4/3/13 8:42 PM, mu xiaojia wrote:
> Sorry for the typo, the last evidence"4) I also compared the generated
> files' sizes, A = B in trr, edr , gro, cpt, if B crashes before reaching
> 100ns, the size would **NOT*** be the same as A."
>

You probably have a corrupted frame.  The simulation continued and the .trr file 
continued being written, so you see comparable file sizes.

-Justin

>
> On Wed, Apr 3, 2013 at 7:25 PM, mu xiaojia <muxiaojia2010 at gmail.com> wrote:
>
>> Dear GMX users,
>>
>> I am not sure if someone has similar problems before. I cannot read half
>> of the frames from trr file after md simulation, and I believe my
>> simulation has already completed.
>>
>> I have finished simulations A and B with both gmx4.5.4 and gmx4.5.5. the
>> only difference between A and B is they are npt simulations under different
>> temperature (in mdp file, "ref_t" part )and such difference would not cause
>> crash of the simulation. I have successfully finished A, everything looks
>> perfect (frames can be successfully extracted), but for B, I could not
>> extract last 70ns' frames from trr.
>>
>> 1) My command is like: mdrun_mpi -s -deffnm MD_A -cpi -append, because I
>> am using super computer so the job will be restarted for multiple times.
>>
>> 2) both simulation are 100ns, both log files indicate that they have
>> finished 100ns simulations. I checked my screen out put for B, whenever it
>> restarted, the output on screen is correct and continuously ( something
>> like: 100000000 steps, 100000.0 ps (continuing from step 95963500,  95963.5
>> ps).
>>
>> 3) With gmxcheck, it looks that my B simulation only reached 29,7ns(which
>> means only the first two restart simulation were recorded into trr, which
>> log files are not saying in this way.)
>> *
>> *
>> *For system A (the successful one), it shows*
>> Reading frame       0 time    0.000
>> # Atoms  72166
>> Last frame     2000 time 100000.000
>>
>>
>> Item        #frames Timestep (ps)
>> Step           2001    50
>> Time           2001    50
>> Lambda       2001    50
>> Coords         2001    50
>> Velocities     2001    50
>> Forces           0
>> Box            2001    50
>>
>> *for system B (the failed one)*
>> Reading frame       0 time    0.000
>> # Atoms  72166
>> Reading frame     500 time 25000.000
>>
>>
>> Item        #frames Timestep (ps)
>> Step           596    50
>> Time           596    50
>> Lambda         596    50
>> Coords         596    50
>> Velocities     596    50
>> Forces           0
>> Box            596    50
>>
>> 4) I also compared the generated files' sizes, A = B in trr, edr , gro,
>> cpt, if B crashes before reaching 100ns, the size would be the same as A.
>>
>> I am wondering what was wrong with my trr file of B . I appreciate for any
>> suggestions!
>>
>> Sincerely
>>
>> Xiaojia
>>
>>

-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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